The battle of wills between Japanese whalers and environmentalists in the Antarctic took a dramatic turn yesterday when two members of the marine conservation group Sea Shepherd were detained by the crew of the harpoon ship they had climbed aboard.

Their detention came hours after a federal court in Sydney ordered Japan to end this year's kill of almost 1,000 whales, ruling the hunt illegal because of it being conducted in Australia's exclusive economic zone.

Giles Lane, a Briton, along with Benjamin Potts, an Australian, were held after boarding the ship named Yushin Maru No. 2, in the Southern Ocean. Their intention was to deliver a letter calling on the fleet to end its "illegal" hunt. Lane, 35, wrote in the letter: "It is my intent to deliver this message and then to request that you allow me to disembark from your vessel without harm or seizure."

The two sides offered wildly conflicting accounts of the incident, with Sea Shepherd claiming the crew had tried to throw 36-year-old Lane overboard before strapping him and Potts, 28, to a radar mast with plastic cord.

The Institute of Cetacean Research, a government body in Tokyo which organises the hunts, said the men had not been harmed and were held in a locked room on the ship for their own safety.

"Any accusations that we have tied them up or assaulted them are completely untrue," the institute's director general, Minoru Morimoto, said. "It is illegal to board another country's vessels on the high seas. As a result, at this stage they are being held in custody while decisions are made on their future." Morimoto claimed the men had boarded the vessel after attempting to entangle its crew and throwing bottles of acid on to the deck.

In another move expected to heighten tensions between Tokyo and anti-whaling countries, Japan, which does not recognise Canberra's territorial claims in the region, said it would ignore yesterday's court decision.

"It is impossible for the Japanese government to accept the Australian court's ruling," Tomohiko Taniguchi, a foreign ministry spokesman, told the Guardian. "As far as we are concerned, Japan's whaling activities are taking place in international waters and under a legal framework set out by the International Whaling Commission. But at this point it is very important that there is no violence on either side and that the activities must be allowed to continue in a calm and peaceful manner."

The whaling fleet says it will slaughter 935 minke and 50 fin whales by mid-April, although it agreed last month to drop plans to catch 50 humpback whales, classed as endangered by some countries, following diplomatic protests by more than 30 nations.

The IWC banned commercial whaling in 1986 but allows Japan to conduct lethal research and sell the meat on the domestic market, a practice critics condemn as a front for commercial whaling. Japan has slaughtered more than 7,000 Antarctic minkes since the moratorium began. In 2004 the Humane Society International sought an injunction preventing the Japanese whaling firm Kyodo Senpaku Kaisha from whaling in Australia's exclusive economic zone. The federal court hearing was derailed a year later following an intervention by the Australian government, which feared it could sour relations with Tokyo, but resumed in 2006 on the orders of the federal court's full bench.

Yesterday the federal court judge James Allsop said the whalers had "killed, injured, taken or interfered with" Antarctic minke and fin whales in the Australian whale sanctuary, but the ruling was unenforceable as the whalers were outside Australian jurisdiction.

The ruling has forced Australia's prime minister, Kevin Rudd, into a political balancing act. Though his Labour party took office in November vowing to take a tougher stance against the whalers than his conservative predecessor, John Howard, he is expected to avoid angering Japan, an important ally.

Last week the Australian government dispatched the Oceanic Viking, an armed surveillance ship, to gather evidence that could be used in a legal challenge to the hunt, but opposition MPs and campaigners accused Rudd of half measures.

Nicola Beynon, a spokeswoman for the Humane Society, said the ship, which is moving towards the hunting grounds, should intercept the whalers and uphold yesterday's court order. "The government can intercept the ship and stop this hunt," she said in Sydney. "It would be controversial with the Japanese government, but they are the ones who are being extremely provocative in killing whales in Australian territorial waters."

Australia's attorney general, Robert McClelland, said interference in the fleet's activities would inflame the volatile situation and put lives at risk.

At the weekend, the whalers had to halt their hunt when their mother ship, the Nisshin Maru, became separated from the fleet in a high-speed chase with the Greenpeace ship Esperanza. The Nisshin Maru, which processes captured whales, is believed to be nearly 400 miles north-west of the other ships.

"They're just running away," Paul Watson, Sea Shepherd's founder, told the Guardian from the ship Steve Irwin. "They seem to be worried we will attack them, but they are the real eco-terrorists. They terrorise the environment."

The Japanese government routinely describes Sea Shepherd as a terrorist organisation, last year accusing it of ramming a whaling vessel and attacking the mother ship with acid.

This week Watson pledged to "hound these poachers" for as long as possible.

Greenpeace is said to disapprove of Sea Shepherd's methods, reportedly refusing to share information about the whaling fleet's activities. A Greenpeace spokesman declined to comment.

Sea Shepherd, meanwhile, called on Britain and Australia to demand the release of the two men and said it had reported the "kidnapping" to Australian police. "The Japanese vessel doesn't seem to be making any attempt to return the men," said Jonny Vasic, Sea Shepherd's international director. "They are basically being held captive."